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- PDB-3mj9: Crystal structure of JAML in complex with the stimulatory antibod... -

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Basic information

Entry
Database: PDB / ID: 3mj9
TitleCrystal structure of JAML in complex with the stimulatory antibody HL4E10
Components
  • Junctional adhesion molecule-like
  • STIMULATORY HAMSTER ANTIBODY HL4E10 FAB HEAVY CHAIN
  • STIMULATORY HAMSTER ANTIBODY HL4E10 FAB LIGHT CHAIN
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN TANDEM DOMAIN / RECEPTOR-ANTIBODY COMPLEX / CELL ADHESION / CELL JUNCTION / GLYCOPROTEIN / IMMUNOGLOBULIN DOMAIN / MEMBRANE / COSTIMULATION / HAMSTER IgG / TRANSMEMBRANE
Function / homology
Function and homology information


monocyte extravasation / gamma-delta T cell activation / neutrophil extravasation / positive regulation of epithelial cell proliferation involved in wound healing / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / bicellular tight junction / cell adhesion molecule binding / neutrophil chemotaxis / integrin binding / protein homodimerization activity ...monocyte extravasation / gamma-delta T cell activation / neutrophil extravasation / positive regulation of epithelial cell proliferation involved in wound healing / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / bicellular tight junction / cell adhesion molecule binding / neutrophil chemotaxis / integrin binding / protein homodimerization activity / integral component of membrane / plasma membrane
Immunoglobulin subtype 2 / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Junctional adhesion molecule-like / Myelin P0 protein-related / Immunoglobulin-like fold / Immunoglobulin subtype / Immunoglobulin-like domain / Immunoglobulins / Immunoglobulin-like ...Immunoglobulin subtype 2 / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Junctional adhesion molecule-like / Myelin P0 protein-related / Immunoglobulin-like fold / Immunoglobulin subtype / Immunoglobulin-like domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Junctional adhesion molecule-like / polysac:dmanpa1-3[dmanpa1-6]dmanpb1-4dglcpnacb1-4[lfucpa1-6]dglcpnacb1-:
Biological speciesMus musculus (house mouse)
CRICETULUS MIGRATORIUS (Armenian hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsVerdino, P. / Wilson, I.A.
CitationJournal: Structure / Year: 2011
Title: Molecular insights into gamma delta T cell costimulation by an anti-JAML antibody.
Authors: Verdino, P. / Witherden, D.A. / Ferguson, M.S. / Corper, A.L. / Schiefner, A. / Havran, W.L. / Wilson, I.A.
Validation Report
SummaryFull reportAbout validation report
History
DepositionApr 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Junctional adhesion molecule-like
L: STIMULATORY HAMSTER ANTIBODY HL4E10 FAB LIGHT CHAIN
H: STIMULATORY HAMSTER ANTIBODY HL4E10 FAB HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5856
Polymers77,0853
Non-polymers1,4993
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7600 Å2
ΔGint-3 kcal/mol
Surface area30250 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)125.020, 125.020, 107.839
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Junctional adhesion molecule-like / / Dendritic cell-specific protein CREA7 / mCrea7


Mass: 30647.387 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN (UNP RESIDUES 21-280) / Mutation: K124R, R211Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Amica1, Gm638, Jaml / Plasmid: PMT/BIP/V5-HIS A / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q80UL9
#2: Antibody STIMULATORY HAMSTER ANTIBODY HL4E10 FAB LIGHT CHAIN


Mass: 22784.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: HL4E10-SECRETING HYBRIDOMA WAS PRODUCED BY FUSING MOUSE MYELOMA CELLS WITH SPLEEN CELLS FROM AN ARMENIAN HAMSTER IMMUNIZED WITH 7-17 DETC
Source: (natural) CRICETULUS MIGRATORIUS (Armenian hamster) / Strain: HYBRIDOMA
#3: Antibody STIMULATORY HAMSTER ANTIBODY HL4E10 FAB HEAVY CHAIN


Mass: 23653.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: HL4E10-SECRETING HYBRIDOMA WAS PRODUCED BY FUSING MOUSE MYELOMA CELLS WITH SPLEEN CELLS FROM AN ARMENIAN HAMSTER IMMUNIZED WITH 7-17 DETC
Source: (natural) CRICETULUS MIGRATORIUS (Armenian hamster) / Strain: HYBRIDOMA
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.2-1.4 M NA-MALONATE, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 22, 2006
Details: SI(111) DOUBLE CRYSTAL MONOCHROMATOR. ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY
RadiationMonochromator: DOUBLE CRYSTAL CRYO-COOLED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.95→30 Å / Num. obs: 18365 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 6.8
Reflection shellResolution: 2.95→3.06 Å / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.617 / % possible all: 99

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.4.0069refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→30 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.875 / SU B: 42.292 / SU ML: 0.358 / Cross valid method: THROUGHOUT / ESU R Free: 0.473 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.287 927 5.1 %RANDOM
Rwork0.222 ---
Obs0.225 17200 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.244 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å20 Å20 Å2
2---1.23 Å20 Å2
3---2.46 Å2
Refinement stepCycle: LAST / Resolution: 2.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4995 0 99 0 5094
Refine LS restraints
Refinement-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225217
X-RAY DIFFRACTIONr_bond_other_d0.0010.023452
X-RAY DIFFRACTIONr_angle_refined_deg1.0611.9687109
X-RAY DIFFRACTIONr_angle_other_deg1.3033.0038421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1385644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.30824.408211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48215844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6681524
X-RAY DIFFRACTIONr_chiral_restr0.0660.2829
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215696
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02994
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2145
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0250.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.238
X-RAY DIFFRACTIONr_symmetry_vdw_other0.150.2105
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.60633219
X-RAY DIFFRACTIONr_mcbond_other0.07131310
X-RAY DIFFRACTIONr_mcangle_it1.21755231
X-RAY DIFFRACTIONr_scbond_it1.98271998
X-RAY DIFFRACTIONr_scangle_it3.516111878
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.95→3.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.48 72 -
Rwork0.295 1246 -
Obs--98.95 %
Refinement TLS params.

Method: refined / Refinement-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.5050.59420.98682.4241.179210.2021-0.05290.04180.14730.0031-0.00790.1462-0.1466-0.23870.0608-0.36650.0280.107-0.17010.1443-0.1724-12.5149-56.1071-16.8211
22.65070.5765-0.09013.31781.68329.87660.0128-0.1190.60090.59170.21060.2432-0.6346-0.5688-0.2234-0.04360.12460.307-0.28580.1071-0.0688-5.6331-33.74130.5488
39.8096-0.6537-0.54055.71291.64984.15530.31460.0910.22450.955-0.1948-0.4588-0.23090.2154-0.1198-0.1259-0.05570.0436-0.44290.1665-0.297917.223-32.6237-15.4424
44.1748-1.10670.98963.19220.27810.7383-0.28150.33480.05570.07470.2846-0.77960.04470.401-0.0031-0.0998-0.2063-0.04560.0049-0.23180.246337.3773-44.5855-46.8504
55.21080.4218-2.22132.7162-2.14999.933-0.18440.90780.36160.0830.40350.4913-0.2921-0.4859-0.2191-0.38270.09680.0882-0.07040.1896-0.13193.8831-28.0776-32.563
64.1028-1.89010.561210.0859-0.27814.08640.06920.1445-0.548-0.16190.2135-0.21910.3971-0.2934-0.2827-0.126-0.2723-0.07080.3302-0.0431-0.207421.3906-47.0282-48.0561
Refinement TLS group
IDRefinement-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 121
2X-RAY DIFFRACTION1A301 - 506
3X-RAY DIFFRACTION2A122 - 236
4X-RAY DIFFRACTION3L2 - 108
5X-RAY DIFFRACTION4L109 - 212
6X-RAY DIFFRACTION5H1 - 113
7X-RAY DIFFRACTION6H114 - 228

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